Name: rs6011149
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs6011149

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:63811886 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.428664 (113463/264690, TOPMED)
A=0.423318 (59240/139942, GnomAD)
G=0.44487 (12571/28258, 14KJPN) (+ 17 more)
A=0.39009 (7485/19188, ALFA)
G=0.44535 (7464/16760, 8.3KJPN)
A=0.4533 (2903/6404, 1000G_30x)
A=0.4499 (2253/5008, 1000G)
A=0.3540 (1586/4480, Estonian)
A=0.3729 (1437/3854, ALSPAC)
A=0.3557 (1319/3708, TWINSUK)
G=0.4154 (1217/2930, KOREAN)
G=0.4061 (744/1832, Korea1K)
A=0.397 (396/998, GoNL)
A=0.413 (248/600, NorthernSweden)
G=0.328 (126/384, SGDP_PRJ)
A=0.417 (90/216, Qatari)
G=0.467 (98/210, Vietnamese)
A=0.41 (34/82, Ancient Sardinia)
A=0.38 (15/40, GENOME_DK)
G=0.33 (10/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZBTB46 : Intron Variant
ZBTB46-AS1 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	19188	G=0.60991	A=0.39009
European	Sub	14286	G=0.64140	A=0.35860
African	Sub	2970	G=0.4492	A=0.5508
African Others	Sub	114	G=0.377	A=0.623
African American	Sub	2856	G=0.4520	A=0.5480
Asian	Sub	116	G=0.440	A=0.560
East Asian	Sub	88	G=0.45	A=0.55
Other Asian	Sub	28	G=0.39	A=0.61
Latin American 1	Sub	154	G=0.604	A=0.396
Latin American 2	Sub	616	G=0.683	A=0.317
South Asian	Sub	98	G=0.74	A=0.26
Other	Sub	948	G=0.599	A=0.401

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.571336	A=0.428664
gnomAD - Genomes	Global	Study-wide	139942	G=0.576682	A=0.423318
gnomAD - Genomes	European	Sub	75798	G=0.63985	A=0.36015
gnomAD - Genomes	African	Sub	41922	G=0.45057	A=0.54943
gnomAD - Genomes	American	Sub	13630	G=0.62472	A=0.37528
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.6429	A=0.3571
gnomAD - Genomes	East Asian	Sub	3126	G=0.4440	A=0.5560
gnomAD - Genomes	Other	Sub	2148	G=0.5950	A=0.4050
14KJPN	JAPANESE	Study-wide	28258	G=0.44487	A=0.55513
Allele Frequency Aggregator	Total	Global	19188	G=0.60991	A=0.39009
Allele Frequency Aggregator	European	Sub	14286	G=0.64140	A=0.35860
Allele Frequency Aggregator	African	Sub	2970	G=0.4492	A=0.5508
Allele Frequency Aggregator	Other	Sub	948	G=0.599	A=0.401
Allele Frequency Aggregator	Latin American 2	Sub	616	G=0.683	A=0.317
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.604	A=0.396
Allele Frequency Aggregator	Asian	Sub	116	G=0.440	A=0.560
Allele Frequency Aggregator	South Asian	Sub	98	G=0.74	A=0.26
8.3KJPN	JAPANESE	Study-wide	16760	G=0.44535	A=0.55465
1000Genomes_30x	Global	Study-wide	6404	G=0.5467	A=0.4533
1000Genomes_30x	African	Sub	1786	G=0.4127	A=0.5873
1000Genomes_30x	Europe	Sub	1266	G=0.6224	A=0.3776
1000Genomes_30x	South Asian	Sub	1202	G=0.7171	A=0.2829
1000Genomes_30x	East Asian	Sub	1170	G=0.4470	A=0.5530
1000Genomes_30x	American	Sub	980	G=0.603	A=0.397
1000Genomes	Global	Study-wide	5008	G=0.5501	A=0.4499
1000Genomes	African	Sub	1322	G=0.4092	A=0.5908
1000Genomes	East Asian	Sub	1008	G=0.4484	A=0.5516
1000Genomes	Europe	Sub	1006	G=0.6382	A=0.3618
1000Genomes	South Asian	Sub	978	G=0.717	A=0.283
1000Genomes	American	Sub	694	G=0.604	A=0.396
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6460	A=0.3540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6271	A=0.3729
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6443	A=0.3557
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4154	A=0.5846
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4061	A=0.5939
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.603	A=0.397
Northern Sweden	ACPOP	Study-wide	600	G=0.587	A=0.413
SGDP_PRJ	Global	Study-wide	384	G=0.328	A=0.672
Qatari	Global	Study-wide	216	G=0.583	A=0.417
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.467	A=0.533
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	82	G=0.59	A=0.41
The Danish reference pan genome	Danish	Study-wide	40	G=0.62	A=0.38
Siberian	Global	Study-wide	30	G=0.33	A=0.67

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 20	NC_000020.11:g.63811886G>A
GRCh37.p13 chr 20	NC_000020.10:g.62443239G>A

Gene: ZBTB46, zinc finger and BTB domain containing 46 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZBTB46 transcript variant 1	NM_001369741.1:c.-34+1921… NM_001369741.1:c.-34+19211C>T	N/A	Intron Variant
ZBTB46 transcript variant 2	NM_025224.4:c.	N/A	Genic Upstream Transcript Variant
ZBTB46 transcript variant X2	XM_005260197.5:c.-34+2006… XM_005260197.5:c.-34+20063C>T	N/A	Intron Variant
ZBTB46 transcript variant X5	XM_005260198.5:c.-34+1881… XM_005260198.5:c.-34+18812C>T	N/A	Intron Variant
ZBTB46 transcript variant X4	XM_006723700.4:c.-34+1867… XM_006723700.4:c.-34+18671C>T	N/A	Intron Variant
ZBTB46 transcript variant X1	XM_011528548.3:c.-34+2009… XM_011528548.3:c.-34+20099C>T	N/A	Intron Variant
ZBTB46 transcript variant X10	XM_011528549.3:c.-34+1921… XM_011528549.3:c.-34+19211C>T	N/A	Intron Variant
ZBTB46 transcript variant X9	XM_017027667.2:c.-34+1921… XM_017027667.2:c.-34+19211C>T	N/A	Intron Variant
ZBTB46 transcript variant X7	XM_047439901.1:c.-34+1223… XM_047439901.1:c.-34+12233C>T	N/A	Intron Variant
ZBTB46 transcript variant X6	XM_005260195.5:c.	N/A	Genic Upstream Transcript Variant
ZBTB46 transcript variant X8	XR_001754167.2:n.	N/A	Intron Variant
ZBTB46 transcript variant X3	XR_936500.3:n.	N/A	Intron Variant

Gene: ZBTB46-AS1, ZBTB46 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZBTB46-AS1 transcript	NR_110081.1:n.	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	G=	A
GRCh38.p14 chr 20	NC_000020.11:g.63811886=	NC_000020.11:g.63811886G>A
GRCh37.p13 chr 20	NC_000020.10:g.62443239=	NC_000020.10:g.62443239G>A
ZBTB46 transcript variant 1	NM_001369741.1:c.-34+19211=	NM_001369741.1:c.-34+19211C>T
ZBTB46 transcript variant X2	XM_005260196.1:c.-34+19211=	XM_005260196.1:c.-34+19211C>T
ZBTB46 transcript variant X3	XM_005260197.1:c.-34+20063=	XM_005260197.1:c.-34+20063C>T
ZBTB46 transcript variant X2	XM_005260197.5:c.-34+20063=	XM_005260197.5:c.-34+20063C>T
ZBTB46 transcript variant X4	XM_005260198.1:c.-34+18812=	XM_005260198.1:c.-34+18812C>T
ZBTB46 transcript variant X5	XM_005260198.5:c.-34+18812=	XM_005260198.5:c.-34+18812C>T
ZBTB46 transcript variant X4	XM_006723700.4:c.-34+18671=	XM_006723700.4:c.-34+18671C>T
ZBTB46 transcript variant X1	XM_011528548.3:c.-34+20099=	XM_011528548.3:c.-34+20099C>T
ZBTB46 transcript variant X10	XM_011528549.3:c.-34+19211=	XM_011528549.3:c.-34+19211C>T
ZBTB46 transcript variant X9	XM_017027667.2:c.-34+19211=	XM_017027667.2:c.-34+19211C>T
ZBTB46 transcript variant X7	XM_047439901.1:c.-34+12233=	XM_047439901.1:c.-34+12233C>T

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

72 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8310055	Apr 21, 2003 (114)
2	HGSV	ss78636485	Dec 06, 2007 (129)
3	BCMHGSC_JDW	ss91757308	Mar 24, 2008 (129)
4	BGI	ss106199542	Feb 05, 2009 (130)
5	1000GENOMES	ss112250938	Jan 25, 2009 (130)
6	1000GENOMES	ss113576084	Jan 25, 2009 (130)
7	IGMI-SNU	ss115486000	Feb 05, 2009 (130)
8	ILLUMINA-UK	ss117611725	Feb 14, 2009 (130)
9	ENSEMBL	ss138272804	Dec 01, 2009 (131)
10	GMI	ss156626170	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss170111825	Jul 04, 2010 (132)
12	BUSHMAN	ss203947262	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208658392	Jul 04, 2010 (132)
14	1000GENOMES	ss228453136	Jul 14, 2010 (132)
15	1000GENOMES	ss237902894	Jul 15, 2010 (132)
16	1000GENOMES	ss244058185	Jul 15, 2010 (132)
17	BL	ss255775109	May 09, 2011 (134)
18	GMI	ss283446978	May 04, 2012 (137)
19	GMI	ss287486637	Apr 25, 2013 (138)
20	PJP	ss292599960	May 09, 2011 (134)
21	ILLUMINA	ss536340460	Sep 08, 2015 (146)
22	TISHKOFF	ss566369479	Apr 25, 2013 (138)
23	SSMP	ss662251038	Apr 25, 2013 (138)
24	EVA-GONL	ss994911663	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1082340901	Aug 21, 2014 (142)
26	1000GENOMES	ss1365501899	Aug 21, 2014 (142)
27	DDI	ss1429107441	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1579579076	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1639170515	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1682164548	Apr 01, 2015 (144)
31	EVA_DECODE	ss1698976362	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1809587035	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1938434929	Feb 12, 2016 (147)
34	GENOMED	ss1969172653	Jul 19, 2016 (147)
35	JJLAB	ss2029997804	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2158570164	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2244260661	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2629491365	Nov 08, 2017 (151)
39	GRF	ss2704267550	Nov 08, 2017 (151)
40	GNOMAD	ss2969464612	Nov 08, 2017 (151)
41	SWEGEN	ss3018480717	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3028832378	Nov 08, 2017 (151)
43	CSHL	ss3352598227	Nov 08, 2017 (151)
44	ILLUMINA	ss3628438523	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3685165732	Jul 13, 2019 (153)
46	EVA_DECODE	ss3707320486	Jul 13, 2019 (153)
47	ACPOP	ss3743555385	Jul 13, 2019 (153)
48	EVA	ss3758873356	Jul 13, 2019 (153)
49	PACBIO	ss3788696705	Jul 13, 2019 (153)
50	PACBIO	ss3793580544	Jul 13, 2019 (153)
51	PACBIO	ss3798468015	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3822026589	Jul 13, 2019 (153)
53	EVA	ss3835766968	Apr 27, 2020 (154)
54	EVA	ss3841508416	Apr 27, 2020 (154)
55	EVA	ss3847022257	Apr 27, 2020 (154)
56	SGDP_PRJ	ss3889494598	Apr 27, 2020 (154)
57	KRGDB	ss3939823173	Apr 27, 2020 (154)
58	KOGIC	ss3982649704	Apr 27, 2020 (154)
59	EVA	ss3985891981	Apr 27, 2021 (155)
60	TOPMED	ss5094803320	Apr 27, 2021 (155)
61	TOMMO_GENOMICS	ss5230484827	Apr 27, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5309448962	Oct 16, 2022 (156)
63	EVA	ss5438594737	Oct 16, 2022 (156)
64	HUGCELL_USP	ss5501663018	Oct 16, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5616209663	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5663575579	Oct 16, 2022 (156)
67	TOMMO_GENOMICS	ss5790554205	Oct 16, 2022 (156)
68	YY_MCH	ss5818203209	Oct 16, 2022 (156)
69	EVA	ss5845949859	Oct 16, 2022 (156)
70	EVA	ss5853218368	Oct 16, 2022 (156)
71	EVA	ss5924173514	Oct 16, 2022 (156)
72	EVA	ss5958508629	Oct 16, 2022 (156)
73	1000Genomes	NC_000020.10 - 62443239	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000020.11 - 63811886	Oct 16, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 62443239	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000020.10 - 62443239	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000020.10 - 62443239	Apr 27, 2020 (154)
78	gnomAD - Genomes	NC_000020.11 - 63811886	Apr 27, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000020.10 - 62443239	Apr 27, 2020 (154)
80	KOREAN population from KRGDB	NC_000020.10 - 62443239	Apr 27, 2020 (154)
81	Korean Genome Project	NC_000020.11 - 63811886	Apr 27, 2020 (154)
82	Northern Sweden	NC_000020.10 - 62443239	Jul 13, 2019 (153)
83	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000020.10 - 62443239	Apr 27, 2021 (155)
84	Qatari	NC_000020.10 - 62443239	Apr 27, 2020 (154)
85	SGDP_PRJ	NC_000020.10 - 62443239	Apr 27, 2020 (154)
86	Siberian	NC_000020.10 - 62443239	Apr 27, 2020 (154)
87	8.3KJPN	NC_000020.10 - 62443239	Apr 27, 2021 (155)
88	14KJPN	NC_000020.11 - 63811886	Oct 16, 2022 (156)
89	TopMed	NC_000020.11 - 63811886	Apr 27, 2021 (155)
90	UK 10K study - Twins	NC_000020.10 - 62443239	Oct 12, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000020.10 - 62443239	Jul 13, 2019 (153)
92	ALFA	NC_000020.11 - 63811886	Apr 27, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78636485, ss91757308, ss112250938, ss113576084, ss117611725, ss170111825, ss203947262, ss208658392, ss255775109, ss283446978, ss287486637, ss292599960, ss1698976362	NC_000020.9:61913682:G:A	NC_000020.11:63811885:G:A	(self)
78990499, 43736402, 30903980, 5744015, 19476814, 47000567, 16840250, 1117908, 20476851, 41511578, 11086518, 88454134, 43736402, 9644244, ss228453136, ss237902894, ss244058185, ss536340460, ss566369479, ss662251038, ss994911663, ss1082340901, ss1365501899, ss1429107441, ss1579579076, ss1639170515, ss1682164548, ss1809587035, ss1938434929, ss1969172653, ss2029997804, ss2158570164, ss2629491365, ss2704267550, ss2969464612, ss3018480717, ss3352598227, ss3628438523, ss3685165732, ss3743555385, ss3758873356, ss3788696705, ss3793580544, ss3798468015, ss3835766968, ss3841508416, ss3889494598, ss3939823173, ss3985891981, ss5230484827, ss5438594737, ss5663575579, ss5845949859, ss5958508629	NC_000020.10:62443238:G:A	NC_000020.11:63811885:G:A	(self)
103735598, 557053454, 39027705, 124391309, 369912265, 9621170409, ss2244260661, ss3028832378, ss3707320486, ss3822026589, ss3847022257, ss3982649704, ss5094803320, ss5309448962, ss5501663018, ss5616209663, ss5790554205, ss5818203209, ss5853218368, ss5924173514	NC_000020.11:63811885:G:A	NC_000020.11:63811885:G:A	(self)
ss8310055	NT_011333.5:1179868:G:A	NC_000020.11:63811885:G:A	(self)
ss106199542, ss115486000, ss138272804, ss156626170	NT_011333.6:1179869:G:A	NC_000020.11:63811885:G:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs6011149

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs6011149